modules/pairix

a tool for indexing and querying on a block-compressed text file containing pairs of genomic coordinates

indexblock-compressedpairs

https://github.com/nf-core/modules/[...]/modules/nf-core/pairix

Description

a tool for indexing and querying on a block-compressed text file containing pairs of genomic coordinates

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`pair`
`:file`

pair file

Output

name:type

description

pattern

`index`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`pair`
`:file`

pair index file

*.px2

`*.px2`
`:file`

pair index file

*.px2

`versions_pairix`

`${task.process}`
`:string`

The name of the process

`pairix`
`:string`

The name of the tool

`pairix --help 2>&1 | sed -n 's/^Version: //p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`pairix`
`:string`

The name of the tool

`pairix --help 2>&1 | sed -n 's/^Version: //p'`
`:eval`

The expression to obtain the version of the tool

Tools

pairix
MIT

2D indexing on bgzipped text files of paired genomic coordinates

github.com/4dn-dcic/pairix

modules/pairix

Description

Input

`meta`
`:map`

`pair`
`:file`

Output

`index`

`meta`
`:map`

`pair`
`:file`

`*.px2`
`:file`

`versions_pairix`

`${task.process}`
`:string`

`pairix`
`:string`

`pairix --help 2>&1 | sed -n 's/^Version: //p'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`pairix`
`:string`

`pairix --help 2>&1 | sed -n 's/^Version: //p'`
`:eval`

Tools

pairix
MIT

included in

maintainer

get in touch

modules/pairix

Description

Input

meta :map

pair :file

Output

index

meta :map

pair :file

*.px2 :file

versions_pairix

${task.process} :string

pairix :string

pairix --help 2>&1 | sed -n 's/^Version: //p' :eval

Topics

versions

${task.process} :string

pairix :string

pairix --help 2>&1 | sed -n 's/^Version: //p' :eval

Tools

pairixMIT

included in

maintainer

get in touch

`meta`
`:map`

`pair`
`:file`

`index`

`meta`
`:map`

`pair`
`:file`

`*.px2`
`:file`

`versions_pairix`

`${task.process}`
`:string`

`pairix`
`:string`

`pairix --help 2>&1 | sed -n 's/^Version: //p'`
`:eval`

`versions`

`${task.process}`
`:string`

`pairix`
`:string`

`pairix --help 2>&1 | sed -n 's/^Version: //p'`
`:eval`

pairix
MIT